The independent MP, who could be kicked out of her seat in May, supported a motion which allows Parliament to organise a series of indicative votes to find out what kind of Brexit has most support among MPs.
Conservative North West Cambridgeshire MP Shailesh Vara opposed the motion, which passed by 329 votes to 302.
Thirty Tory MPs voted against the Government, including three ministers - Richard Harrington, Alistair Burt and Steve Brine - who resigned to join the rebels.
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Indicative votes on a range of different options to break the Brexit impasse will be voted on tomorrow (Wednesday, March 27).
However, the votes are not binding on the Government and Prime Minister Theresa May said she may not follow the wishes of Parliament.
The motion had been put forward by Conservative MP Oliver Letwin and Labour MP Hilary Benn.
Conservative rebels included Grantham and Stamford MP Nick Boles and Huntingdon MP Jonathan Djanogly.
Brexit Secretary and MP for North East Cambridgeshire Steve Barclay, South Holland and The Deepings MP John Hayes and Corby MP Tom Pursglove all voted against the motion.
Ms Onasanya also supported an amendment from Labour MP Margaret Beckett to allow MPs a vote on a no deal Brexit or to request an extension should the UK come within seven days of leaving the EU without a deal.
However, that amendment was rejected by 314 votes to 311.
Mr Vara, Mr Barclay, Mr Hayes and Mr Pursglove all voted against the Beckett amendment.
Mr Boles and Mr Djanogly both supported it.
A recall petition which could see Ms Onasanya lose her seat is currently running in Peterborough after she was jailed for perverting the course of justice. If 10 per cent of her constituents (nearly 7,000) sign it by 5pm on May 1 a by-election will be triggered.
The MP said this morning: “Last night as amendment A was carried (the vote was successful) on Weds we, as the House, will now be able to set out the direction of travel through a series of indicative votes so keep your emails letters coming through.”